Mercurial > repos > jeremyjliu > region_motif_enrichment
comparison region-motif-compare/region_motif_intersect.xml @ 17:7afdfd4f4c1b draft
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author | jeremyjliu |
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date | Wed, 12 Nov 2014 15:21:11 -0500 |
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16:9a84f76db861 | 17:7afdfd4f4c1b |
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1 <tool id="region_motif_intersect" name="Region Motif Intersect"> | |
2 <description>for computing the motifs that lie inside a region set</description> | |
3 <requirements> | |
4 <requirement type="set_environment">RMOTIF_PATH</requirement> | |
5 </requirements> | |
6 <command interpreter="Rscript"> | |
7 region_motif_intersect.r --args \$RMOTIF_PATH $db_type $in_bed $out_tab | |
8 </command> | |
9 <inputs> | |
10 <param name="in_bed" type="data" format="bed" label="Input BED File" /> | |
11 <param name="db_type" type="select" label="Select Motif Database" > | |
12 <option value="t">Test Pouya Subset (hg19)</option> | |
13 <option value="p">Pouya Encode Motifs (hg19)</option> | |
14 <option value="j">Jaspar and Jolma Motifs (hg19)</option> | |
15 <option value="m">Mouse Motifs (mm9)</option> | |
16 </param> | |
17 </inputs> | |
18 <outputs> | |
19 <data name="out_tab" format="tabular" /> | |
20 </outputs> | |
21 | |
22 <help> | |
23 This tool computes the motifs and the number of motifs that intersect | |
24 any region in a input set of regions. | |
25 </help> | |
26 | |
27 </tool> |